The best place at the end of the body tag, like
some html body tags
.
.
.
If you do like so, then the html will load quicker and main pros is that all your ids and classes will get assigned otherwise sometime if you put script above html, then there might be a chance that you try to get an element by id that is not yet assigned in DOM
[UPDATE]
Here is an example code that Bootstrap is using in their own website: http://getbootstrap.com/getting-started/
you can find this code under Basic template Heading:
Bootstrap 101 Template
Hello, world!